Data, Stats and Daily Numbers started 18th January 2022

[boys3]

Welcome to another instalment of the DATA thread.

Our preference is for factual, data driven and analytical contributions.
Please try to keep discussion focused on these

UK govt press conferences slides & data www.gov.uk/government/collections/slides-and-datasets-to-accompany-coronavirus-press-conferences#history
UKHSA Variants of Concern Technical Briefings www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefing
UKHSA Vaccine efficacy www.gov.uk/guidance/monitoring-reports-of-the-effectiveness-of-covid-19-vaccination
SAGE : Minutes and Models www.gov.uk/government/collections/scientific-evidence-supporting-the-government-response-to-coronavirus-covid-19
Data Dashboard coronavirus.data.gov.uk/ includes R estimates
UKHSA Weekly Flu & Covid Surveiilance Reports 2021-22 Season www.gov.uk/government/statistics/national-flu-and-covid-19-surveillance-reports-2021-to-2022-season
Dashboard Vaccine Map to MSOA level coronavirus.data.gov.uk/details/interactive-map/vaccinations
Covid 19 Genomics www.cogconsortium.uk/tools-analysis/public-data-analysis-2/
Sanger Genome Maps & Data covid19.sanger.ac.uk/lineages/raw
UCL Virus Watch ucl-virus-watch.net/
NHS Vaccination data www.england.nhs.uk/statistics/statistical-work-areas/covid-19-vaccinations/
Sewage www.gov.uk/government/publications/wastewater-testing-coverage-data-for-19-may-2021-emhp-programme/wastewater-testing-coverage-data-for-the-environmental-monitoring-for-health-protection-emhp-programme.
Sewage reports www.gov.uk/government/publications/monitoring-of-sars-cov-2-rna-in-england-wastewater-monthly-statistics-june-2021
Global vaccination data ourworldindata.org/covid-vaccinations
R estimates UK & English regions www.gov.uk/guidance/the-r-number-in-the-uk
Imperial UK weekly LAs, cases / 100k, table, map, hotspots statistics imperialcollegelondon.github.io/covid19local/#map
NHS England Hospital activity www.england.nhs.uk/statistics/statistical-work-areas/covid-19-hospital-activity/
NHS England Daily deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/
Cases Tracker England Local Government lginform.local.gov.uk/reports/view/lga-research/covid-19-case-tracker
ONS MSOA Map English deaths www.england.nhs.uk/statistics/statistical-work-areas/covid-19-daily-deaths/

Scot gov Daily data www.gov.scot/publications/coronavirus-covid-19-daily-data-for-scotland/
Scotland TravellingTabby LAs, care homes, hospitals, tests, t&t www.travellingtabby.com/scotland-coronavirus-tracker/
PH Wales LAs, cases, tests, deaths Dashboard public.tableau.com/profile/public.health.wales.health.protection#!/vizhome/RapidCOVID-19virology-Public/Headlinesummary
ICNRC Intensive Care National Audit & Research reports www.icnarc.org/Our-Audit/Audits/Cmp/Reports
NHS t&t England & UK testing Weekly stats www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
PHE Surveillance reports & LA Local Watchlist Maps by LSOA (from last summer) www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports
ONS England infection surveillance report each Friday www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/bulletins/coronaviruscovid19infectionsurveypilot/previousReleases
Datasets for ONS surveillance reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/coronaviruscovid19infectionsurveydata/2020
ONS Roundup deaths, infections & economic reports www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19roundup/2020-03-26
Zoe UK data covid.joinzoe.com/data#interactive-map
ECDC (European Centre for Disease Control rolling 14-day incidence EEA & UK www.ecdc.europa.eu/en/cases-2019-ncov-eueea

Worldometer UK page www.worldometers.info/coronavirus/country/uk/
Our World in Data GB test positivity etc, DIY country graphs ourworldindata.org/coronavirus/country/united-kingdom?country=~GBR
FT DIY graphs compare deaths, cases, raw / million pop ig.ft.com/coronavirus-chart/?areas=eur&areas=usa&areas=bra&areas=gbr&areas=cze&areas=hun&areasRegional=usny&areasRegional=usnj&areasRegional=usaz&areasRegional=usca&areasRegional=usnd&areasRegional=ussd&cumulative=0&logScale=0&per100K=1&startDate=2020-09-01&values=deaths

PHE local health data fingertips.phe.org.uk/profile/health-profiles
Alama Personal COVID risk assessment alama.org.uk/covid-19-medical-risk-assessment/
Local Mobility Reports for countries www.google.com/covid19/mobility/
UK Highstreet Tracker for cities & large towns Footfall, spend index, workers, visitors, economic recovery www.centreforcities.org/data/high-streets-recovery-tracker/

I don't think masks in schools was ever really about protecting kids from catching covid as an end in itself. They'll mostly catch it at some point, masks just slow that time down a bit. The reason for requiring masks was about trying to do all that was possible to slow the spread across wider society to avoid excessive demand in the NHS all at once. The data that the government is looking at when they decide to remove the need for masks is the hospital numbers. That's what it's always been most about.

@wintertravel1980

First of all, many CEV people were vaccinated early, in September or October in many cases, so immunity is waning now.

There is supposed to be a plan with antivirals - in theory. In practice, it is proving very hard to put this in place and many people who ought to be eligible are finding they cannot access this easily or indeed at all.

It is quite difficult even for immunosuppressed young people to access a booster.

It seems a bit foolish to start removing mitigations before more of this has been sorted out, while we are still in maybe the biggest wave of the pandemic, with several hundred deaths per day, over 100k positive tests daily and probably still a seven figure number with covid in the UK.

Although we can't at this point keep covid out of schools altogether, the lower the better as far as cases are concerned, from the point of view of reducing disruption. Especially as reinfections are 16 times more common with omicron, so getting it once is not getting it over with.

Of course, the big question is around CEV population but people boosted before Christmas should now be at their peak immunity. At an individual level, people infected in January might have a better health outcome than if they catch Covid 3 months later

But,@wintertravel1980, the CEV started receiving boosters in September/October didn't they, not just before Christmas?

But,**@wintertravel1980, the CEV started receiving boosters in September/October didn't they, not just before Christmas?

Yes, sorry, a very fair point.

October boosters should still hold up (US data suggests protection lasts at least 3 months) but September is a question mark.

Interesting thread with various dashboard/stats points from the new Lead. Starts with effects of pausing need for confirmatory PCRs:

twitter.com/statsgeekclare/status/1484226977653567493?s=21

Thinking about it, a decision to “speed up the spread” in January might have been driven by concerns about waning immunity for people boosted in September.

I am not sure the government is that rational though.

Re: the 16-fold risk of re-infection - this related to protection from old variants (from WT to Delta). Most epidemiologists seem to believe that the Omicron infection should protect against Omicron. We do not yet have real life data.

[quote JanglyBeads]Interesting thread with various dashboard/stats points from the new Lead. Starts with effects of pausing need for confirmatory PCRs:

twitter.com/statsgeekclare/status/1484226977653567493?s=21[/quote]
Certainly suggests all the fuss about people not registering LFTs was unfounded doesn't it? LFT cases remaining pretty constant while PCR cases decline. I suspect many people with symptoms too are just getting LFTs - they're so much quicker and easier to get hold of.

An interesting thread on Denmark.
mobile.twitter.com/JosetteSchoenma/status/1484190295453581314

Thinking about it, the last thing we want to do right now is speed up the spread.

@wintertravel1980

Thinking about it, a decision to “speed up the spread” in January might have been driven by concerns about waning immunity for people boosted in September.

I am not sure the government is that rational though.

Re: the 16-fold risk of re-infection - this related to protection from old variants (from WT to Delta). Most epidemiologists seem to believe that the Omicron infection should protect against Omicron. We do not yet have real life data.

I don’t see why it wouldn’t be a consideration

Because it is a crazy idea?

Speeding up the spread will put vulnerable people at more risk and put more pressure on the health service, at the peak risk time for problems with flu and RSV.

Why would anyone in their right mind want to do that?

I don’t agree it’s crazy to take boosters waning into consideration

As someone CEV, I had my booster in October. There is research evidence suggest a good effect; with evidence also suggesting waning after 10 weeks.

On balance, I would very much prefer not to get covid right now, and I would like the effect of boosters waning to be taken into account by continuing with protective measures over the next couple of months.

That would be the logical outcome of taking into account the effect of boosters waning.,

Protective measures are not cost free some will want them to continue but other pressures to release.

It sounds like you’re good at avoiding it so far though and cases falling rapidly

The only reason to change direction right at this point is Johnson's party politics.

Otherwise we are still in winter, still with sky high cases - over 100k yesterday - still with pressure on the NHS, still with hundreds of deaths a day and rising. None of that has changed in such a way as to support lowering restrictions at this point.

Cases are falling

This is my London borough. We will be ahead but that sharp peak will be replicated in other areas

Well first off, London is very different to the situation elsewhere.

And secondly, we want rates to continue to fall if possible, and this isn't the way to help that happen.

I doubt that is due to measures if it was France and other countries with more in place than us wouldn’t still be rising higher.

Previous infection and a peak is what will create that shape

If measures were working it’d be a bit shallower not cause a drop

still with hundreds of deaths a day and rising

This is being looked at and needs to change in the way it is reported. ONS now reports significantly less deaths than the government website due to the 28 day rule, and the prevalance of Omicron.

At the stage we are at, and with Omicron, the daily data we are seeing is no longer fit for purpose. It needs to be more nuanced, which is a big ask in terms of NHS reporting, which is generally pretty basic and not very timely.

I read something today about the rate of re infections being effectively ignored but it’s been long established that we can get covid twice?

Will have a dig.

Iggly No the rate of reinfections is not ignored, it's just not possible to update the dashboard to easily deal with it (remember there's not some handy single database of people and covid, there's a massive job of linking together tests and people and de-duplicating, you don't want to count a single persons LFT, the PCR, the day 6 and 7 LFT's the additional PCR on hospital entry all as "new cases", so you need to de-dupe, de-duping all was the easiest way to do it, when re-infections numbered in the tens or hundreds. So that's the dashboard.

Welsh data is distinct and has a simpler rule where by any two tests 28 days apart are new cases, so there re-infections are counted.

Similar exercises on the England data is done and published in the weekly, there's also a huge data dump on the type of individual in www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/datasets/coronaviruscovid19infectionsinthecommunityinengland
and also of note that re-infection viral load (as defined by cycle threshold on the pcr) is considerably less in the re-infection)

The excess deaths are in the negative at the minute for the age groups 0-49 and the over 75s
The 50 -64 age group seem the hardest hit currently with their excess deaths coming also from other causes.
Cancer is showing as in a negative across age groups, which I read as being just not possible so they thought cases are being missed. Eg lung cancer 7% decrease.

I agree with the way deaths are reported. Looking at the dashboard to deaths to date of death it is actually fairly consistently around the 200-250 mark - yes high, yes probably higher than it should be but we havent had over 300 since February last year - so not hundreds per day. Although the 15th onwards still could be added to that.

The issue is though that it is reported in a haphazard way so that the last 3 days look incredibly high 330, 359, 438 because they are adding to the 85 and 91 the previous days. This I think can skew perception - both ways. The lower days that it is ok and the higher days that it is growing. Whereas the average 260 looks actually to be what it is.

www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19latestinsights/infections

So the commonest discriminator of symptoms in Omicron with around 43% people reporting are "no symptoms", just beating cough on around 38%, this is different to delta where no symptoms and cough were similar.

Loss of taste/smell has really disappeared with omicron, however there's nothing that seems to have replaced it, sore throat the only commoner symptom, but I suspect like others that would be a very low quality discriminator given how common it is with other things.

And secondly, we want rates to continue to fall if possible, and this isn't the way to help that happen.

James Ward previously ran a range of scenarios that showed that suppressing cases below a certain (pretty high) threshold will only (i) lead to a higher wave a few months down the road and (ii) increase negative health outcomes at the population level.

I think we have all got used to “stop/slow down the spread” mantra but it might no longer be the optimal strategy if we are close to endemic equilibrium. While we do want cases to fall in comparison to the Dec peak, we should expect some pretty high level of baseline transmission. It is highly unlikely to be 1,000 or 10,000 cases a day. With Delta some scientists were talking about 20,000-60,000 cases. With Omicron the number is likely to be higher.

Re: individual risks - it is a tough call. I certainly do not advise that anyone tries to proactively get Covid. However it is useful to keep assessing the balance of risks (time from the booster shot, availability of antrivirals - Pavloxid, etc).